Reading vti

Thiago Franco de Moraes
1 parent 4e527a1a
Showing 3 changed files with 80 additions and 2 deletions Show diff stats
invesalius/control.py
invesalius/data/imagedata_utils.py
invesalius/reader/vtk_reader.py
@@ -33,6 +33,7 @@ import data.volume as volume
 import gui.dialogs as dialog
 import project as prj
 import reader.analyze_reader as analyze
+import reader.vtk_reader as vtk_reader
 import reader.dicom_grouper as dg
 import reader.dicom_reader as dcm
 import session as ses
@@ -351,8 +352,12 @@ class Controller():
                 self.CreateAnalyzeProject(imagedata)
             # OPTION 3: Nothing...
             else:
-                utils.debug("No medical images found on given directory")
-                return
+                imagedata = vtk_reader.ReadDirectory(directory)
+                if imagedata:
+                    self.CreateVTKProject(imagedata)
+                else:
+                    utils.debug("No medical images found on given directory")
+                    return
         self.LoadProject()
         Publisher.sendMessage("Enable state project", True)
  
@@ -414,6 +419,44 @@ class Controller():
  
         Publisher.sendMessage('End busy cursor')
  
+    def CreateVTKProject(self, imagedata):
+        proj = prj.Project()
+        proj.imagedata = None
+        proj.name = _("Untitled")
+        proj.SetAcquisitionModality("CT")
+        #TODO: Verify if all Analyse are in AXIAL orientation
+
+        # To get  Z, X, Y (used by InVesaliu), not X, Y, Z
+
+        proj.threshold_range = imagedata.GetScalarRange()
+        proj.window = proj.threshold_range[1] - proj.threshold_range[0]
+        proj.level =  (0.5 * (proj.threshold_range[1] + proj.threshold_range[0]))
+        proj.spacing = imagedata.GetSpacing()
+        proj.matrix_shape = imagedata.GetDimensions()[::-1]
+        proj.original_orientation =  const.AXIAL
+
+        matrix, matrix_filename = image_utils.vtk2mmap(imagedata)
+        proj.matrix_dtype = matrix.dtype.name
+        proj.matrix_filename = matrix_filename
+
+        self.Slice = sl.Slice()
+        self.Slice.matrix = matrix
+        self.Slice.matrix_filename = matrix_filename
+
+        self.Slice.window_level = proj.level
+        self.Slice.window_width = proj.window
+        self.Slice.spacing = proj.spacing
+
+        session = ses.Session()
+        filename = proj.name+".inv3"
+
+        filename = filename.replace("/", "") #Fix problem case other/Skull_DICOM
+
+        dirpath = session.CreateProject(filename)
+
+        Publisher.sendMessage('Update threshold limits list',
+                                   proj.threshold_range)
+
     def CreateAnalyzeProject(self, imagedata):
         header = imagedata.get_header()
         proj = prj.Project()
@@ -493,6 +493,16 @@ def dcm2memmap(files, slice_size, orientation, resolution_percentage):
  
     return matrix, scalar_range, temp_file
  
+def vtk2mmap(imagedata):
+    temp_file = tempfile.mktemp()
+    shape = imagedata.GetDimensions()[::-1]
+    array = numpy_support.vtk_to_numpy(imagedata.GetPointData().GetScalars())
+    array.shape = shape
+    matrix = numpy.memmap(temp_file, mode='w+', dtype='int16', shape=shape)
+    matrix[:] = array
+    matrix.flush()
+    return matrix, temp_file
+
 def analyze2mmap(analyze):
     data = analyze.get_data()
     header = analyze.get_header()
@@ -0,0 +1,25 @@
+import os
+import multiprocessing
+import tempfile
+
+import vtk
+
+def ReadVTK(filename):
+    r = vtk.vtkXMLImageDataReader()
+    r.SetFileName(filename)
+    r.Update()
+
+    return r.GetOutput()
+
+def ReadDirectory(dir_):
+    """ 
+    Looking for analyze files in the given directory
+    """
+    imagedata = None
+    for root, sub_folders, files in os.walk(dir_):
+        for file in files:
+            if file.split(".")[-1] == "vti":
+                filename = os.path.join(root,file)
+                imagedata = ReadVTK(filename)
+                return imagedata
+    return imagedata
...	...	@@ -33,6 +33,7 @@ import data.volume as volume
33	33	import gui.dialogs as dialog
34	34	import project as prj
35	35	import reader.analyze_reader as analyze
	36	+import reader.vtk_reader as vtk_reader
36	37	import reader.dicom_grouper as dg
37	38	import reader.dicom_reader as dcm
38	39	import session as ses
...	...	@@ -351,8 +352,12 @@ class Controller():
351	352	self.CreateAnalyzeProject(imagedata)
352	353	# OPTION 3: Nothing...
353	354	else:
354		- utils.debug("No medical images found on given directory")
355		- return
	355	+ imagedata = vtk_reader.ReadDirectory(directory)
	356	+ if imagedata:
	357	+ self.CreateVTKProject(imagedata)
	358	+ else:
	359	+ utils.debug("No medical images found on given directory")
	360	+ return
356	361	self.LoadProject()
357	362	Publisher.sendMessage("Enable state project", True)
358	363
...	...	@@ -414,6 +419,44 @@ class Controller():
414	419
415	420	Publisher.sendMessage('End busy cursor')
416	421
	422	+ def CreateVTKProject(self, imagedata):
	423	+ proj = prj.Project()
	424	+ proj.imagedata = None
	425	+ proj.name = _("Untitled")
	426	+ proj.SetAcquisitionModality("CT")
	427	+ #TODO: Verify if all Analyse are in AXIAL orientation
	428	+
	429	+ # To get Z, X, Y (used by InVesaliu), not X, Y, Z
	430	+
	431	+ proj.threshold_range = imagedata.GetScalarRange()
	432	+ proj.window = proj.threshold_range[1] - proj.threshold_range[0]
	433	+ proj.level = (0.5 * (proj.threshold_range[1] + proj.threshold_range[0]))
	434	+ proj.spacing = imagedata.GetSpacing()
	435	+ proj.matrix_shape = imagedata.GetDimensions()[::-1]
	436	+ proj.original_orientation = const.AXIAL
	437	+
	438	+ matrix, matrix_filename = image_utils.vtk2mmap(imagedata)
	439	+ proj.matrix_dtype = matrix.dtype.name
	440	+ proj.matrix_filename = matrix_filename
	441	+
	442	+ self.Slice = sl.Slice()
	443	+ self.Slice.matrix = matrix
	444	+ self.Slice.matrix_filename = matrix_filename
	445	+
	446	+ self.Slice.window_level = proj.level
	447	+ self.Slice.window_width = proj.window
	448	+ self.Slice.spacing = proj.spacing
	449	+
	450	+ session = ses.Session()
	451	+ filename = proj.name+".inv3"
	452	+
	453	+ filename = filename.replace("/", "") #Fix problem case other/Skull_DICOM
	454	+
	455	+ dirpath = session.CreateProject(filename)
	456	+
	457	+ Publisher.sendMessage('Update threshold limits list',
	458	+ proj.threshold_range)
	459	+
417	460	def CreateAnalyzeProject(self, imagedata):
418	461	header = imagedata.get_header()
419	462	proj = prj.Project()
...	...
...	...	@@ -493,6 +493,16 @@ def dcm2memmap(files, slice_size, orientation, resolution_percentage):
493	493
494	494	return matrix, scalar_range, temp_file
495	495
	496	+def vtk2mmap(imagedata):
	497	+ temp_file = tempfile.mktemp()
	498	+ shape = imagedata.GetDimensions()[::-1]
	499	+ array = numpy_support.vtk_to_numpy(imagedata.GetPointData().GetScalars())
	500	+ array.shape = shape
	501	+ matrix = numpy.memmap(temp_file, mode='w+', dtype='int16', shape=shape)
	502	+ matrix[:] = array
	503	+ matrix.flush()
	504	+ return matrix, temp_file
	505	+
496	506	def analyze2mmap(analyze):
497	507	data = analyze.get_data()
498	508	header = analyze.get_header()
...	...
...	...	@@ -0,0 +1,25 @@
	1	+import os
	2	+import multiprocessing
	3	+import tempfile
	4	+
	5	+import vtk
	6	+
	7	+def ReadVTK(filename):
	8	+ r = vtk.vtkXMLImageDataReader()
	9	+ r.SetFileName(filename)
	10	+ r.Update()
	11	+
	12	+ return r.GetOutput()
	13	+
	14	+def ReadDirectory(dir_):
	15	+ """
	16	+ Looking for analyze files in the given directory
	17	+ """
	18	+ imagedata = None
	19	+ for root, sub_folders, files in os.walk(dir_):
	20	+ for file in files:
	21	+ if file.split(".")[-1] == "vti":
	22	+ filename = os.path.join(root,file)
	23	+ imagedata = ReadVTK(filename)
	24	+ return imagedata
	25	+ return imagedata
...	...